7-10241816-G-T

Variant names:

• chr7-10241816-G-T
• rs7785107

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.116 in 151,712 control chromosomes in the GnomAD database, including 1,896 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17579 AN: 151594 Hom.: 1892 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0344

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0835

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.116 AC: 17602 AN: 151712 Hom.: 1896 Cov.: 32 AF XY: 0.114 AC XY: 8443 AN XY: 74186

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0344

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.0807

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0826

Alfa AF: 0.0498 Hom.: 162

Bravo AF: 0.121

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.0
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7785107; hg19: chr7-10281443;